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lammps/doc/special_bonds.txt
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
special_bonds command :h3
[Syntax:]
special_bonds style
special_bonds c1 c2 c3
special_bonds c1 c2 c3 c4 c5 c6 :pre
style = {charmm} or {amber}
c1,c2,c3,c4,c5,c6 = numeric coefficients from 0.0 to 1.0 :ul
Examples:
special_bonds charmm
special_bonds amber
special_bonds 0.0 0.0 1.0
special_bonds 0.0 0.0 1.0 0.0 0.0 0.5 :pre
[Description:]
Set the weighting coefficients for the pairwise force and energy
contributions from atom pairs that are also bonded to each other
directly or indirectly. The 1st coefficient is the weighting factor
on 1-2 atom pairs, which are those directly bonded to each other. The
2nd coefficient is the weighting factor on 1-3 atom pairs which are
those separated by 2 bonds (e.g. the 2 H atoms in a water molecule).
The 3rd coefficient is the weighting factor on 1-4 atom pairs which
are separated by 3 bonds (e.g. the 1st and 4th atoms in a dihedral
interaction).
Note that for purposes of computing weighted pairwise interactions,
1-3 and 1-4 interactions are not defined from the list of angles or
dihedrals used by the simulation. Rather, they are inferred
topologically by the set of bonds defined when atoms are read in from
a file ("read_data"_read_data.html or
"read_restart"_read_restart.html). Thus the set of 1-2,1-3,1-4
interactions is the same whether angle potentials are computed or not,
and remains the same even if bonds are constrained, or turned off, or
removed during a simulation. The only exception is if the
"delete_bonds"_delete_bonds.html command is used with the {special}
option that recomputes the 1-2,1-3,1-4 topologies; see the command for
more details.
The {charmm} style sets all 3 coefficients to 0.0, which is the
default for the CHARMM force field. In pair styles
{lj/charmm/coul/charmm} and {lj/charmm/coul/long} the 1-4 coefficients
are defined explicitly, and these pair-wise contributions are computed
in the charmm dihedral style - see the "pair_coeff"_pair_coeff.html
and "dihedral_style"_dihedral_style.html commands for more
information.
The {amber} style sets the 3 coefficients to 0.0 0.0 0.5 for LJ
interactions and to 0.0 0.0 0.833 for Coulombic interactions, which is
the default for a particular version of the AMBER force field, where
the last value is 5/6.
A special_bonds command with 3 coefficients sets the 1-2, 1-3, and 1-4
coefficients for both LJ and Coulombic terms to those values.
A special_bonds command with 6 coefficients sets the 1-2, 1-3, and 1-4
LJ coefficients to the first 3 values and the Coulombic coefficients
to the last 3 values.
[Restrictions:] none
[Related commands:]
"delete_bonds"_delete_bonds.html
[Default:]
special_bonds 0.0 0.0 0.0 :pre
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